rs7691494

Variant names:

• chr4-5940922-C-G
• rs7691494
• ENST00000639345.1:n.*2673+15780G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000639345.1(C4orf50):​n.*2673+15780G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,030 control chromosomes in the GnomAD database, including 5,417 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.24 (5417 hom., cov: 32)
• Consequence: C4orf50 ENST00000639345.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.766
• Publications: 2 publications found

Genes affected

C4orf50 (HGNC:33766): (chromosome 4 open reading frame 50)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C4orf50	XM_047415663.1	c.*1807-12353G>C		intron_variant	Intron 13 of 14		XP_047271619.1
C4orf50	XM_047415664.1	c.*2673+15780G>C		intron_variant	Intron 12 of 12		XP_047271620.1
C4orf50	XM_047415667.1	c.*2674-12353G>C		intron_variant	Intron 11 of 12		XP_047271623.1
C4orf50	XM_017008893.2	c.*1807-12353G>C		intron_variant	Intron 11 of 12		XP_016864382.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C4orf50	ENST00000639345.1	n.*2673+15780G>C		intron_variant	Intron 7 of 7	5		ENSP00000492340.1

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35902 AN: 151912 Hom.: 5405 Cov.: 32

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.0399

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.233

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.236 AC: 35944 AN: 152030 Hom.: 5417 Cov.: 32 AF XY: 0.227 AC XY: 16899 AN XY: 74330

African (AFR) AF: 0.426 AC: 17654 AN: 41446

American (AMR) AF: 0.165 AC: 2523 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 850 AN: 3468

East Asian (EAS) AF: 0.0398 AC: 206 AN: 5174

South Asian (SAS) AF: 0.112 AC: 538 AN: 4818

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12114 AN: 67968

Other (OTH) AF: 0.231 AC: 487 AN: 2108

Alfa AF: 0.207 Hom.: 478

Bravo AF: 0.249

Asia WGS AF: 0.113 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.70
PhyloP100		-0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7691494; hg19: chr4-5942649;